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- PDB-1a0a: PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1a0a
TitlePHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX
Components
  • DNA (5'-D(*CP*TP*AP*GP*TP*CP*CP*CP*AP*CP*GP*TP*GP*TP*GP*AP*G )-3')
  • DNA (5'-D(*CP*TP*CP*AP*CP*AP*CP*GP*TP*GP*GP*GP*AP*CP*TP*AP*G )-3')
  • PROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION FACTOR / BASIC HELIX LOOP HELIX / COMPLEX (TRANSCRIPTION FACTOR-DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of phosphate metabolic process / cellular response to phosphate starvation / sequence-specific DNA binding / protein dimerization activity / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Phosphate system positive regulatory protein PHO4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsShimizu, T. / Toumoto, A. / Ihara, K. / Shimizu, M. / Kyogoku, Y. / Ogawa, N. / Oshima, Y. / Hakoshima, T.
CitationJournal: EMBO J. / Year: 1997
Title: Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition.
Authors: Shimizu, T. / Toumoto, A. / Ihara, K. / Shimizu, M. / Kyogoku, Y. / Ogawa, N. / Oshima, Y. / Hakoshima, T.
History
DepositionNov 27, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*CP*TP*CP*AP*CP*AP*CP*GP*TP*GP*GP*GP*AP*CP*TP*AP*G )-3')
D: DNA (5'-D(*CP*TP*AP*GP*TP*CP*CP*CP*AP*CP*GP*TP*GP*TP*GP*AP*G )-3')
A: PROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4)
B: PROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4)


Theoretical massNumber of molelcules
Total (without water)24,6244
Polymers24,6244
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.510, 68.300, 108.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*CP*TP*CP*AP*CP*AP*CP*GP*TP*GP*GP*GP*AP*CP*TP*AP*G )-3') / UASP2(17)


Mass: 5212.386 Da / Num. of mol.: 1 / Fragment: UPSTREAM ACTIVATION SITE P2 / Source method: obtained synthetically / Keywords: FRAGMENT UPSTREAM ACTIVATION SITE P2
#2: DNA chain DNA (5'-D(*CP*TP*AP*GP*TP*CP*CP*CP*AP*CP*GP*TP*GP*TP*GP*AP*G )-3') / UASP2(17)


Mass: 5203.373 Da / Num. of mol.: 1 / Fragment: UPSTREAM ACTIVATION SITE P2 / Source method: obtained synthetically / Keywords: FRAGMENT: UPSTREAM ACTIVATION SITE P2
#3: Protein PROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4) / BHLH


Mass: 7104.062 Da / Num. of mol.: 2 / Fragment: DNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Keywords: FRAGMENT: DNA BINDING DOMAIN / References: UniProt: P07270
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 71 %
Crystal growMethod: vapor diffusion / pH: 3.6
Details: VAPOR DIFFUSION METHOD: DROP-0.4MM PROTEIN, 0.2MM DNA, 1% PEG6K, 20MM NACITRATE (PH3.6), RESERVOIR-1% PEG6K, 20MM NACITRATE(PH3.6), vapor diffusion
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2NA CITRATE11
3PEG 600012
4NA CITRATE12
Crystal
*PLUS
Density % sol: 71 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.4 mMprotein1drop
20.2 mMDNA1drop
31 %(w/v)PEG60001drop
420 mMsodium citrate1drop
51 %(w/v)PEG60001reservoir
620 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.8 Å / Num. obs: 9398 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 4.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 3.5 / % possible all: 80.4
Reflection
*PLUS
Highest resolution: 2.8 Å / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Num. measured all: 36943 / Biso Wilson estimate: 26.2 Å2
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.95 Å / % possible obs: 76.8 % / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.1refinement
WEISdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.8→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.284 948 12.5 %RANDOM
Rwork0.23 ---
obs-7581 77.3 %-
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--3.9 Å20 Å2
3----3.34 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 691 0 80 1767
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.42
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.78
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→2.92 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.319 86 13.1 %
Rwork0.257 569 -
obs--54.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM_NDBX.DNAETOP_NDBX.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 12.5 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.78
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / % reflection Rfree: 13.1 %

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